CHEM 1406 Concept Review: Amino Acids, Proteins, and Enzymes

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Amino Acids

Amino Acids: molecules composed of a central “alpha carbon” bonded to a carboxylate group (), an ammonium group (), and one of a variety of different side-chains.  These molecules serve as the building blocks of proteins. 

General Amino Acid Structure:

 Amino Acid Structure.png

 

 

Classification of Amino Acids Table
Amino Acid Classification Table.png

 

 

D vs. L Stereoisomers of Amino Acids

D vs L amino acid.png

 

 

Amino Acids as Acids and Bases

Isoelectric Point: the pH at which an amino acid has an overall neutral charge (charge = 0).  The most stable form of this is called the zwitterion form in which the carboxylic acid group loses its acidic hydrogen and is negatively charged and the basic amino group has gained a hydrogen and is positively charged.  See below:

Effect of pH on amino acids.png

*At high pH, there are numerous OH- ions in solution which react with the ammonium group (-NH3+) and remove an H+ from it, converting it into the “anion” form shown above.

**At low pH, there are numerous H+ ions which react with the carboxylate group (-COO-), donating an H+ to it and converting it into the “cation” form shown above.

Below the Isoelectric Point

 

Above the Isoelectric Point

 The amino acid behaves like a base, accepting an H+

 

The amino acid behaves like an acid, donating an H+

The carboxylate group (-COO-) becomes a carboxylic acid group (-COOH)

 

The ammonium group (-NH3+) becomes an amine group (NH2)

The amino acid has an overall positive charge

 

The amino acid has an overall negative charge

 

 

Proteins

Protein: a polymer or combination of polymers composed of amino acids linked together by peptide bonds.

Peptide bonds: Amide bonds that link together the nitrogen of one amino acid to the carboxylic acid group of another amino acid.

Every polypeptide chain has an end with an amino (-NH2)/ammonium group (-NH3+).  The amino acid at this end is called the N-terminal amino acid.  At the opposite end of the peptide chain is a carboxylate (-COO-)/ carboxylic acid (-COOH) group.  The amino acid at this carboxyl end is called the C-terminal amino acid.

 

Naming Peptides

When naming peptides, start with the N-terminal amino acid and proceed across the chain towards the C-terminal amino acid.  All of the amino acids except the C-terminal amino acid have the “-ine” ending changed into “–yl.”  The C-terminal amino acid keeps its name unchanged. See example below:

Naming Peptide Chains img.png

Name:  Glycyllysylserylaspartylglycine

(Gly-Lys-Ser-Asp-Gly)

 

Levels of Protein Structure
Levels of Protein Structure Table.png

 

 

Effects of Protein Denaturing Agents
Effects of Denaturing Agents Table.png

 

 

Enzymes

Enzymes: biological catalysts that are needed for most chemical reactions in the body to take place fast enough to support life

Enzyme-Substrate Complex: the complex that forms when an enzyme binds to a substrate (reactant) to catalyze a reaction with that substrate.

Enzyme Substrate Complex.png

 

Models of Enzyme Activity

Lock and Key Model

 

Induced-Fit Model

In this model of enzyme activity, the active site of the enzyme is seen as being rigid and inflexible, similar to a lock.  The substrate can be seen as a key that specifically fits that lock.

 

 

In this model of enzyme activity, the active site of the enzyme is seen as flexible, allowing it to adapt to the shape of the substrate.  In addition, the substrate itself can be modified to better fit the geometry of the active site.



Factors Affecting Enzyme Activity
Factors Affecting Enzyme Activity Table.png